I want to make a search for all .fits files that contain a certain text in their name and then copy them to a directory.
I can use a command called fetchKeys to list the files that contain say 'foo'
The command looks like this : fetchKeys -t 'foo' -F | grep .fits
This returns a list of .fits files that contain 'foo'. Great! Now I want to copy all of these to a directory /path/to/dir. There are too many files to do individually , I need to copy them all using one command.
I'm thinking something like:
fetchKeys -t 'foo' -F | grep .fits > /path/to/dir
or
cp fetchKeys -t 'foo' -F | grep .fits /path/to/dir
but of course neither of these works. Any other ideas?
If this is on Linux/Unix, can you use the find command? That seems very much like fetchkeys.
$ find . -name "*foo*.fit" -type f -print0 | while read -r -d $'\0' file
do
basename=$(basename $file)
cp "$file" "$fits_dir/$basename"
done
The find command will find all files that match *foo*.fits in their name. The -type f says they have to be files and not directories. The -print0 means print out the files found, but separate them with the NUL character. Normally, the find command will simply return a file on each line, but what if the file name contains spaces, tabs, new lines, or even other strange characters?
The -print0 will separate out files with nulls (\0), and the read -d $'\0' file means to read in each file separating by these null characters. If your files don't contain whitespace or strange characters, you could do this:
$ find . -name "*foo*.fit" -type f | while read file
do
basename=$(basename $file)
cp "$file" "$fits_dir/$basename"
done
Basically, you read each file found with your find command into the shell variable file. Then, you can use that to copy that file into your $fits_dir or where ever you want.
Again, maybe there's a reason to use fetchKeys, and it is possible to replace that find with fetchKeys, but I don't know that fetchKeys command.
Copy all files with the name containing foo to a certain directory:
find . -name "*foo*.fit" -type f -exec cp {} "/path/to/dir/" \;
Copy all files themselves containing foo to a certain directory (solution without xargs):
for f in `find . -type f -exec grep -l foo {} \;`; do cp "$f" /path/to/dir/; done
The find command has very useful arguments -exec, -print, -delete. They are very robust and eliminate the need to manually process the file names. The syntax for -exec is: -exec (what to do) \;. The name of the file currently processed will be substituted instead of the placeholder {}.
Other commands that are very useful for such tasks are sed and awk.
The xargs tool can execute a command for every line what it gets from stdin. This time, we execute a cp command:
fetchkeys -t 'foo' -F | grep .fits | xargs -P 1 -n 500 --replace='{}' cp -vfa '{}' /path/to/dir
xargs is a very useful tool, although its parametrization is not really trivial. This command reads in 500 .fits files, and calls a single cp command for every group. I didn't tested it to deep, if it doesn't go, I'm waiting your comment.
Related
I am trying to grep 40k files in the current directory and i am getting this error.
for i in $(cat A01/genes.txt); do grep $i *.kaks; done > A01/A01.result.txt
-bash: /usr/bin/grep: Argument list too long
How do one normally grep thousands of files?
Thanks
Upendra
This makes David sad...
Everyone so far is wrong (except for anubhava).
Shell scripting is not like any other programming language because much of the interpretation of lines comes from the power of the shell interpolating them before the command is actually executed.
Let's take something simple:
$ set -x
$ ls
+ ls
bar.txt foo.txt fubar.log
$ echo The text files are *.txt
echo The text files are *.txt
> echo The text files are bar.txt foo.txt
The text files are bar.txt foo.txt
$ set +x
$
The set -x allows you to see how the shell actually interpolates the glob and then passes that back to the command as input. The > points to the line that is actually being executed by the command.
You can see that the echo command isn't interpreting the *. Instead, the shell grabs the * and replaces it with the names of the matching files. Then and only then does the echo command actually executes the command.
When you have 40K plus files, and you do grep *, you're expanding that * to the names of those 40,000 plus files before grep even has a chance to execute, and that's where the error message /usr/bin/grep: Argument list too long is coming from.
Fortunately, Unix has a way around this dilemma:
$ find . -name "*.kaks" -type f -maxdepth 1 | xargs grep -f A01/genes.txt
The find . -name "*.kaks" -type f -maxdepth 1 will find all of your *.kaks files, and the -depth 1 will only include files in the current directory. The -type f makes sure you only pick up files and not a directory.
The find command pipes the names of the files into xargs and xargs will append the names of the file to the grep -f A01/genes.txtcommand. However, xargs has a trick up it sleeve. It knows how long the command line buffer is, and will execute the grep when the command line buffer is full, then pass in another series of file to the grep. This way, grep gets executed maybe three or ten times (depending upon the size of the command line buffer), and all of our files are used.
Unfortunately, xargs uses whitespace as a separator for the file names. If your files contain spaces or tabs, you'll have trouble with xargs. Fortunately, there's another fix:
$ find . -name "*.kaks" -type f -maxdepth 1 -print0 | xargs -0 grep -f A01/genes.txt
The -print0 will cause find to print out the names of the files not separated by newlines, but by the NUL character. The -0 parameter for xargs tells xargs that the file separator isn't whitespace, but the NUL character. Thus, fixes the issue.
You could also do this too:
$ find . -name "*.kaks" -type f -maxdepth 1 -exec grep -f A01/genes.txt {} \;
This will execute the grep for each and every file found instead of what xargs does and only runs grep for all the files it can stuff on the command line. The advantage of this is that it avoids shell interference entirely. However, it may or may not be less efficient.
What would be interesting is to experiment and see which one is more efficient. You can use time to see:
$ time find . -name "*.kaks" -type f -maxdepth 1 -exec grep -f A01/genes.txt {} \;
This will execute the command and then tell you how long it took. Try it with the -exec and with xargs and see which is faster. Let us know what you find.
You can combine find with grep like this:
find . -maxdepth 1 -name '*.kaks' -exec grep -H -f A01/genes.txt '{}' \; > A01/A01.result.txt
you can use recursive feature of grep:
for i in $(cat A01/genes.txt); do
grep -r $i .
done > A01/A01.result.txt
though if you want to select only kaks files:
for i in $(cat A01/genes.txt); do
find . -iregex '.*\.kaks$' -exec grep $i \;
done > A01/A01.result.txt
Put another for loop inside your outer one:
for f in *.kaks; do
grep -H $i "$f"
done
By the way, are you interested in finding EVERY occurrence in each file, or merely if the search string exists in there one or more times? If it is "good enough" to know the string occurs in there one or more times you can specify "-n 1" to grep and it will not bother reading/searching the rest of the file after finding the first match, which could potentially save lots of time.
The following solution has worked for me:
Problem:
grep -r "example\.com" *
-bash: /bin/grep: Argument list too long
Solution:
grep -r "example\.com" .
["In newer versions of grep you can omit the “.“, as the current directory is implied."]
Source:
Reinlick, J. https://www.saotn.org/bash-grep-through-large-number-files-argument-list-too-long/
I am having 35K + odd files in multiple directories and subdirectories. There are 1000 odd files (.c .h and other file names) with a unique string "FOO" in the FILE CONTENT. I am trying to copy those files alone (with the directory structure preserved) to a different directory 'MEOW'. Can some one look in to my bash execution and correct my mistake
for Eachfile in `find . -iname "*FOO*" `
do
cp $Eachfile MEOW
done
getting the following error
./baash.sh: line 2: syntax error near unexpected token `$'do\r''
'/baash.sh: line 2: `do
To find all files under the current directory with the string "FOO" in them and copy them to directory MEOW, use:
grep --null -lr FOO . | xargs -0 cp -t MEOW
Unlike find, grep looks in the contents of a file. The -l option to grep tells it to list file names only. The -r option tells it to look recursively in subdirectories. Because file names can have spaces and other odd characters in them, we give the --null option to grep so that, in the list it produces, the file names are safely separated by null characters. xargs -0 reads from that list of null-separated file names and provides them as argument to the command cp -t MEOW which copies them to the target directory MEOW.
In case you only want to search for the string FOO in .c and .h file then
find ./ -name "*\.c" -o -name "*\.h" -exec grep -l FOO {} \; | xargs cp -t MEOW/
For me its working even without --null option to xrags, if doesn't for you.. then append -0 in xargs part as follow:
xargs -0 cp -t MEOW/
for file in $(find -name '*.c' -o -name '*.h' -exec grep -l 'FOO' {} \;); do
dname=$(dirname "$file")
dest="MEOW/$dname"
mkdir -p $dest
cp "$file" "$dest"
done
Basically I have a directory and sub-directories that needs to be scanned to find .csv files. From there I want to copy all lines containing "foo" from the csv's found to new files (in the same directory as the original) but with the name reflecting the file it was found in.
So far I have
find -type f -name "*.csv" | xargs egrep -i "foo" > foo.csv
which yields one backup file (foo.csv) with everything in it, and the location it was found in is part of the data. Both of which I don't want.
What I want:
For example if I have:
csv1.csv
csv2.csv
and they both have lines containing "foo", I would like those lines copied to:
csv1_foo.csv
csv2_foo.csv
and I don't anything extra entered in the backups, other than the full line containing "foo" from the original file. I.e. I don't want the original file name in the backup data, which is what my current code does.
Also, I suppose I should note that I'm using egrep, but my example doesn't use regex. I will be using regex in my search when I apply it to my specific scenario, so this probably needs to be taken into account when naming the new file. If that seems too difficult, an answer that doesn't account for regex would be fine.
Thanks ahead of time!
try this if helps it anyway.
find -type f -name "*.csv" | xargs -I {} sh -c 'filen=`echo {} | sed 's/.csv//' | sed "s/.\///"` && egrep -i "foo" {} > ${filen}_foo.log'
You can try this:
$ find . -type f -exec grep -H foo '{}' \; | perl -ne '`echo $2 >> $1_foo` if /(.*):(.*)/'
It uses:
find to iterate over files
grep to print file path:line tuples (-H switch)
perl to echo those line to the output files (using backslashes, but it could be done prettier).
You can also try:
find -type f -name "*.csv" -a ! -name "*_foo.csv" | while read f; do
grep foo "$f" > "${f%.csv}_foo.csv"
done
I am trying to remove files within a directory. Some of the files have double-quotes around their name while others do not. An example of these files would be:
"DDD344".csv
D2DW.csv
Both these files are located in sub-directories within the directory YM.
To find such files and remove them, I invoke find like so:
find YM -name "*.csv" -print | xargs rm
The above command results in a lot of No such file or directory errors.
I tried using sed in the following way:
find yum/yum_hyd -name "\"*\".csv" | sed 's/"/\"/g' | xargs rm
but to no avail. How do I remove the files?
The problem is that you're using xargs. xargs is a horribly broken program that should never be used for anything except in conjunction with the nonstandard -0 option. Even so, I can't think of any advantages to doing that in this case. You should just execute rm directly from find.
find . -type f -name '"*".csv' -exec rm -f -- {} +
Will work. If you have GNU find, you may also use -delete.
try this:
find yum/yum_hyd -name "\"*\".csv" |sed 's/"/\\"/g'|xargs rm
explanation:
you want to replace " with \". but if you write \" directly, sed considers it as plain ", you have to escape the backslash. so \\" works.
I wasn't aware of this option until recently but you can list the inode of the file in the following way:
$ ls –il
In the output you will see that the first column contains the inode value. You can then use that value to find -inum the offending files and remove them.
Output
2616366 -rw-r--r-- 1 etc etc
$ find . -inum 2616366 -exec rm -f {} \;
This will remove the file with that specific inum.
As a test you can run the following to locate your files.
ls -il \"* | awk '{print $1}' | xargs -n1 -I {} find -inum {}
Replace the final portion of this command (the "find -inum {}") with the "rm" command once you are satisfied.
This is also similar to the question on SuperUser
When I am using xargs sometimes I do not need to explicitly use the replacing string:
find . -name "*.txt" | xargs rm -rf
In other cases, I want to specify the replacing string in order to do things like:
find . -name "*.txt" | xargs -I '{}' mv '{}' /foo/'{}'.bar
The previous command would move all the text files under the current directory into /foo and it will append the extension bar to all the files.
If instead of appending some text to the replace string, I wanted to modify that string such that I could insert some text between the name and extension of the files, how could I do that? For instance, let's say I want to do the same as in the previous example, but the files should be renamed/moved from <name>.txt to /foo/<name>.bar.txt (instead of /foo/<name>.txt.bar).
UPDATE: I manage to find a solution:
find . -name "*.txt" | xargs -I{} \
sh -c 'base=$(basename $1) ; name=${base%.*} ; ext=${base##*.} ; \
mv "$1" "foo/${name}.bar.${ext}"' -- {}
But I wonder if there is a shorter/better solution.
The following command constructs the move command with xargs, replaces the second occurrence of '.' with '.bar.', then executes the commands with bash, working on mac OSX.
ls *.txt | xargs -I {} echo mv {} foo/{} | sed 's/\./.bar./2' | bash
It is possible to do this in one pass (tested in GNU) avoiding the use of the temporary variable assignments
find . -name "*.txt" | xargs -I{} sh -c 'mv "$1" "foo/$(basename ${1%.*}).new.${1##*.}"' -- {}
In cases like this, a while loop would be more readable:
find . -name "*.txt" | while IFS= read -r pathname; do
base=$(basename "$pathname"); name=${base%.*}; ext=${base##*.}
mv "$pathname" "foo/${name}.bar.${ext}"
done
Note that you may find files with the same name in different subdirectories. Are you OK with duplicates being over-written by mv?
If you have GNU Parallel http://www.gnu.org/software/parallel/ installed you can do this:
find . -name "*.txt" | parallel 'ext={/} ; mv -- {} foo/{/.}.bar."${ext##*.}"'
Watch the intro videos for GNU Parallel to learn more:
https://www.youtube.com/playlist?list=PL284C9FF2488BC6D1
If you're allowed to use something other than bash/sh, AND this is just for a fancy "mv"... you might try the venerable "rename.pl" script. I use it on Linux and cygwin on windows all the time.
http://people.sc.fsu.edu/~jburkardt/pl_src/rename/rename.html
rename.pl 's/^(.*?)\.(.*)$/\1-new_stuff_here.\2/' list_of_files_or_glob
You can also use a "-p" parameter to rename.pl to have it tell you what it WOULD HAVE DONE, without actually doing it.
I just tried the following in my c:/bin (cygwin/windows environment). I used the "-p" so it spit out what it would have done. This example just splits the base and extension, and adds a string in between them.
perl c:/bin/rename.pl -p 's/^(.*?)\.(.*)$/\1-new_stuff_here.\2/' *.bat
rename "here.bat" => "here-new_stuff_here.bat"
rename "htmldecode.bat" => "htmldecode-new_stuff_here.bat"
rename "htmlencode.bat" => "htmlencode-new_stuff_here.bat"
rename "sdiff.bat" => "sdiff-new_stuff_here.bat"
rename "widvars.bat" => "widvars-new_stuff_here.bat"
the files should be renamed/moved from <name>.txt to /foo/<name>.bar.txt
You can use rename utility, e.g.:
rename s/\.txt$/\.txt\.bar/g *.txt
Hint: The subsitution syntax is similar to sed or vim.
Then move the files to some target directory by using mv:
mkdir /some/path
mv *.bar /some/path
To do rename files into subdirectories based on some part of their name, check for:
-p/--mkpath/--make-dirs Create any non-existent directories in the target path.
Testing:
$ touch {1..5}.txt
$ rename --dry-run "s/.txt$/.txt.bar/g" *.txt
'1.txt' would be renamed to '1.txt.bar'
'2.txt' would be renamed to '2.txt.bar'
'3.txt' would be renamed to '3.txt.bar'
'4.txt' would be renamed to '4.txt.bar'
'5.txt' would be renamed to '5.txt.bar'
Adding on that the wikipedia article is surprisingly informative
for example:
Shell trick
Another way to achieve a similar effect is to use a shell as the launched command, and deal with the complexity in that shell, for example:
$ mkdir ~/backups
$ find /path -type f -name '*~' -print0 | xargs -0 bash -c 'for filename; do cp -a "$filename" ~/backups; done' bash
Inspired by an answer by #justaname above, this command which incorporates Perl one-liner will do it:
find ./ -name \*.txt | perl -p -e 's/^(.*\/(.*)\.txt)$/mv $1 .\/foo\/$2.bar.txt/' | bash